The purpose of this project is to develop methodology for analyzing molecular population genetic data. We have focused on haplotype analysis and proposed the use of spectral analysis of the pairwise LD matrix to describe haplotype structure for chromosome 12 data for the HAPMAP project. To improve our understanding of the haplotype structure of genes, we have begun a detailed examination of the resequenced data of the Environmental Genome Project (EGP). These data suggest that the current density of the HAPMAP is inadequate if one wants to use the HAPMAP as a resource for candidate gene-association studies.